Fungi in decayed roots of conifer seedlings in forest nurseries, afforested clear‐cuts and abandoned farmland

Abstract

Fungi colonizing decayed roots of Pinus sylvestris and Picea abies seedlings were assessed by pure-culture isolation and direct sequencing of DNA extracted from roots collected from three environments: bare-root forest nurseries; afforested clear-cuts; and abandoned farmland. Pure-culture isolation from 1500 roots collected from 480 seedlings (240 of each tree species) yielded 1110 isolates which, based on mycelial morphology and ITS rDNA sequencing, were found to represent 87 distinct taxa. Direct ITS rDNA sequencing from decayed sections of 140 roots (70 of each tree species) yielded 160 sequences representing 58 taxa. Direct sequencing revealed a significantly higher fungal diversity per root segment than pure-culture isolation. Overall, a total of 131 taxa were found, 92 of which (70·2%) were identified at least to genus level. Only 14 taxa (10·7%) were detected by both methods, while 73 (55·7%) were detected exclusively by isolation and 44 (33·6%), exclusively by sequencing. The pathogens Fusarium oxysporum (25·6%) and Nectria radicicola (14·9%) were the most common isolates. In contrast, direct sequencing most frequently detected endophyte Phialocephala fortinii (33·1%) and Chalara sp. NS234A2 (10·0%). There were no significant differences in species richness between roots from the different environments, but there was a marked effect on fungal community structure. The results demonstrate that different fungi inhabit decayed roots of conifer seedlings in different environments, and that pure-culture isolation and direct sequencing are complementary methods that are both necessary for a complete description of the fungal communities colonizing diseased conifer roots.

High-Throughput Sequencing Shows High Fungal Diversity and Community Segregation in the Rhizospheres of Container-Grown Conifer Seedlings

“…Furthermore, due to the intensive nature of both management and production, forest nurseries are among the most vulnerable environments affected by tree pathogens. Intensive management practices (e.g., large monocultures of densely grown seedlings, intensive fertilization, irrigation, chemical weed and pest control) may often stress plants and create conditions favorable for establishment and rapid spread of fungal infections, resulting in tremendous economical losses [13]. Early detection of such diseases is critical as this can prevent further establishment and spread to new environments.…”

Fungi associated with Ips acuminatus (Coleoptera: Curculionidae) in Ukraine with a special emphasis on pathogenicity of ophiostomatoid species

“…Fungal cultures were divided into groups based on their morphology, and for species identifi cation representative cultures from each group were subjected to sequencing of the internal transcribed spacer regions of the fungal ribosomal RNA (ITS rRNA). Isolation of DNA, amplifi cation and sequencing followed the methods described by Menkis et al (2006). Amplifi cation by PCR was done using primers ITS1F (Gardes &Bruns, 1993) andITS4 (White et al, 1990).…”

Biodiversity of Fungi in Strawberry Fields in Anamur, TURKEY

“…Mucor racemosus is a plant pathogen that can cause allergic reactions in humans [26]. Mucor fragilis is reported as a growth promotor in plants [27]. Fusarium oxysporum is the cause of fusarium wilt disease [28].…”